I've ran into a couple issues regarding control of the ship:
I'll be controlling the ship, but someone else is the captain thus getting the credit for my work as the one maneuvering the ship. I feel like the one on the helm should be the one getting "captain's credit" for broadside hits, as more often than not the actual captain is off just doing crew work and offering no leadership.
The roles will be reversed, and some asshat will have control of the ship. This might work well if the person with control of the ship is someone of equal skill to you that you know and trust, but otherwise it's basically a shit show. I think a captain-exclusive option to take the wheel from whoever is on it (kicking them off the helm) would remedy this issue.
During a match recently we had a shit captain, and every time we voted on a mutiny it just re-elected him. Dunno what that's about.
I may be blind and these might already exist, but servers that only allow players of a certain level and captain nominations for captains with something like 75%+ ratings would be great. It's annoying to have a 100% rating, then a group of low level guys come in and vote on their friend with a 12% rating, thus putting someone completely incompetent in control. Later on down the line, it might be nice to have captain statistics for the crew to look at so they can pick from the captains which already have high ratings. Some extra pre-match time would offset the time it would take to view the stats I suppose.